Variant report

Variant	rs2729631
Chromosome Location	chr12:26200565-26200566
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr12:26200539-26201102	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr12:26200533-26201024	H1-hESC	embryonic stem cell:	n/a	n/a
3	RAD21	chr12:26200540-26201044	H1-hESC	embryonic stem cell:	n/a	chr12:26200547-26200560
4	POLR2A	chr12:26200564-26200904	H1-hESC	embryonic stem cell:	n/a	n/a
5	CREB1	chr12:26200556-26201029	H1-hESC	embryonic stem cell:	n/a	n/a
6	TCF12	chr12:26200475-26200832	H1-hESC	embryonic stem cell:	n/a	n/a
7	YY1	chr12:26200548-26200906	H1-hESC	embryonic stem cell:	n/a	n/a
8	NANOG	chr12:26200545-26200891	H1-hESC	embryonic stem cell:	n/a	n/a
9	RAD21	chr12:26200561-26200936	H1-hESC	embryonic stem cell:	n/a	n/a
10	HDAC2	chr12:26200519-26200914	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
RASSF8	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10459081	0.85[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap]
rs10771250	0.84[CHB][hapmap]
rs10771255	0.85[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.81[ASN][1000 genomes]
rs10842651	0.89[CHB][hapmap];0.81[JPT][hapmap];0.80[YRI][hapmap]
rs10842655	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10842658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842659	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11048363	0.84[CHB][hapmap]
rs12369462	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1513124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1874351	0.85[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs1986802	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1994995	0.94[CHB][hapmap];0.86[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap]
rs2251618	1.00[ASW][hapmap];0.89[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2271483	0.82[ASN][1000 genomes]
rs2643927	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2643930	0.88[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2643933	0.84[LWK][hapmap];0.88[MKK][hapmap];0.96[YRI][hapmap]
rs2729634	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2729635	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61247260	0.81[ASN][1000 genomes]
rs6487522	0.84[CHB][hapmap]
rs7132820	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7136804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7137379	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7138742	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs7139241	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7295585	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7299421	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7956992	0.89[CHB][hapmap];0.87[JPT][hapmap];0.96[YRI][hapmap]
rs7963754	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs7969486	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs7979763	0.84[CHB][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2729631	LRMP	cis	parietal	SCAN
rs2729631	RASSF8	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:26192400-26228600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:26193600-26200600	Weak transcription	Left Ventricle	heart
3	chr12:26195200-26201200	Enhancers	Colon Smooth Muscle	Colon
4	chr12:26195600-26200600	Weak transcription	HUVEC	blood vessel
5	chr12:26196200-26208200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:26196400-26200600	Weak transcription	Fetal Heart	heart
7	chr12:26196400-26201000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:26196400-26219800	Weak transcription	Fetal Kidney	kidney
9	chr12:26196600-26200600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:26196800-26200800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr12:26196800-26201400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:26197000-26201600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr12:26197000-26208200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:26197200-26200600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:26197200-26200600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr12:26197200-26200600	Weak transcription	Placenta	Placenta
17	chr12:26197200-26206000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr12:26197200-26209400	Weak transcription	NHLF	lung
19	chr12:26197200-26211800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:26197200-26228600	Weak transcription	Aorta	Aorta
21	chr12:26197600-26209200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr12:26197800-26201400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr12:26197800-26209000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr12:26198000-26200800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:26198600-26200600	Weak transcription	NH-A	brain
26	chr12:26198800-26200800	Weak transcription	Osteobl	bone
27	chr12:26199000-26200800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr12:26199200-26220200	Weak transcription	Brain Substantia Nigra	brain
29	chr12:26199400-26221600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr12:26199800-26200600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:26199800-26200600	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr12:26199800-26200800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr12:26199800-26201600	Enhancers	H1 Cell Line	embryonic stem cell
34	chr12:26200000-26200600	Enhancers	NHDF-Ad	bronchial
35	chr12:26200000-26200800	Enhancers	Stomach Smooth Muscle	stomach
36	chr12:26200000-26201000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr12:26200000-26201000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:26200000-26201400	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr12:26200000-26205400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr12:26200000-26205800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr12:26200200-26200600	Weak transcription	Fetal Brain Male	brain
42	chr12:26200400-26200600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr12:26200400-26200600	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr12:26200400-26200600	Enhancers	Right Ventricle	heart
45	chr12:26200400-26200800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr12:26200400-26200800	Enhancers	Fetal Muscle Trunk	muscle
47	chr12:26200400-26200800	Enhancers	Lung	lung
48	chr12:26200400-26200800	Enhancers	Pancreas	Pancrea
49	chr12:26200400-26200800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr12:26200400-26201000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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